No Shortcuts
by hermiine
Summary: My version of the missing parts from The Hole in the Heart and The Change in the Game. No spoilers for season 7.
1. Part 1

**No Shortcuts – Part 1**

Booth woke up early the next morning. When he turned to look at his alarm clock to see exactly how early, he realized that he was alone in his bed. He took a deep breath of air that still smelled like her and them and let out a sigh. He wondered what waking up alone meant as he got himself out of the bed and opened the door to the living room. He was relieved to see that at least he wasn't alone in his apartment just yet.

"'Morning," Brennan said giving him a tentative smile when she noticed him watching her sitting on the still made up couch putting on the last one of her socks. Her hair was wet and she looked so beautiful to him, yet he felt a big heavy lump in his stomach.

"'Morning," he said leaning sideways on the doorpost.

"I didn't mean to wake you. You need to be well rested so you can get Broadsky today," she started "I borrowed a towel. Hope that was ok." She nodded towards the still wet towel hanging across one of his chairs.

"Sure," he said "I had hoped you had woken me though. I got worried when you weren't there."

"I think you would have noticed if Broadsky had gotten in here in the middle of the night and taken me," she told him seriously.

"That's not what I was worried about," he looked at her intensely. "I thought you'd left."

"I hadn't," she simply said.

"Not yet," he looked sad. He wasn't sure that he wanted to know, but he needed to know. "Do you regret what happened last night?"

"I … I" she started. She wasn't ready to have this conversation now. But she also knew that she needed to give him something so that he would know that they were ok. "I'm not sure that I'm strong enough for this yet," she said looking down at her hands "Last night I really needed you," she continued as she forced her head up so that her eyes could meet his " Your comfort, I guess, and to feel something other than … But no I don't regret it."

Booth looked at her like he wasn't sure that he could trust what she was saying. He thought that she might just be saying that so he wouldn't feel bad. Although that wasn't really something he expected from Brennan. She always told the truth regardless of the consequences.

When she saw the doubt in his eyes, she got up from the couch and walked over to him.

"Booth, we'll be ok," she said putting her arms around his neck and talking right into his ear. "I need to get to the lab so we can get that evidence and you can get Broadsky."

"Yeah, we'll be ok," he said wanting to believe it. He held on to her tightly and inhaled the scent of his shampoo in her hair. They broke the contact and she picked up her bag. "You need a ride?" he asked.

"No, Hodgins and Angela are swinging by and picking me up on their way," she paused "We arranged that yesterday. They're probably here any minute. We want to get an early start."

She gave him an encouraging smile and turned to walk towards his door. He decided that he had to believe her. That there were no regrets.

ooo

When the vehicle transporting Vincent Nigel-Murrays remains was out of sight they all turned to walk back into the lab. Brennan had linked her arm with Booths and leaned into him as they were the last to follow. Booth had felt proud and reassured when she had showed up with that potted plant. He couldn't help thinking about how far she had come since he first got to know her. How far they had both come.

"I'm glad you came," he told her as he entered the building behind the others. "I didn't doubt that you would, but …"

"I'm relieved to see you're ok," she filled the silence between them "I have the outmost respect for you as an agent and a sniper, you know that. I think you're very good, but I must admit I was afraid that you wouldn't come back from that harbor."

"So was I," he admitted.

They all sat down in the lounge area over the platform and Cam went to her office and came back with a bottle of sparkly rosé wine.

"It was a Christmas present," she said when she noticed Booth looking at her with disbelief "I think it's what we all need right now."

"I sure could have used that right now," Angela agreed.

The rest of them took a glass and with a silent toast they honored their lost friend. They weren't talking much, but they all needed this time together with silent contemplation to start getting some kind of closure. Eventually they started to get up and leave to go home.

"I can give you a ride," Booth said to Brennan when they were the last two remaining.

"That's not necessary. I have my car here since yesterday," she said and started to put her coat back on.

"Bones …" he started protesting.

"Meet you back at my place?" she looked at him with a calm expression on her face.

He sighed with relief and nodded. At least she wasn't running away from him.

"I'll get some take-out on my way over," he said and smiled back at her. He didn't think either one of them had had that much to eat during the day.

ooo

Forty-five minutes later Booth knocked on her door and Brennan came to open up.

"Hi," she was unsure how to greet him. The relief to again see him well and unharmed after everything that had happened the last two days made her want to throw herself in his arms now that they were finally alone, but she simply settled on relieving him from the bags of food.

"Hi," he said back "I might have gone a little bit overboard with the ordering. I didn't realize how hungry I was until I was at that Thai place."

He took off his jacket and hung it up on the coatrack before he followed her into the kitchen

"Do you want to sit here," she nodded towards the kitchen table "or in the living room?"

"It doesn't matter," he shrugged his shoulders and went to get two glasses from the cupboard and started filling them with water.

Brennan started to unpack the continent of the bags he had brought and arrange it all on the kitchen table. They both sat down at the table and started to pick at the food.

"We need to talk," Booth finally said. He was not at all comfortable with the silence.

"I know," Brennan simply said, but not making a motion to start.

"I'm sorry about …" Booth started.

"You have nothing to be sorry about," Brennan protested forcefully.

"I don't?"

"No, you don't. Well not towards me at least," she continued "You asked if I regretted it and I don't, but I guess I didn't ask how you felt about it. Do you regret us having sex last night?"

"No," he said slowly "But I wish things were different between us now."

"Booth, I'm not ready for that," she said knowing she was disappointing him, but unable to say anything else and still be true to herself.

"You want us to go back. Be just friends and partners," he nodded and sighed. In a way he wasn't at all surprised. It was what he had suspected all day. He was only waiting to hear a lecture on human's responses to chock, biological urges, stress related hormones or something like that. But it didn't come.

"I don't think I'm strong enough yet to give you all those things that you want from a relationship. The 30, 40, 50 years, I might never be ready for that."

"But that's no reason to …"

"Do you still want those things?" Brennan interrupted him.

"Yes," he sighed "With you."

"I may never be able to give them to you even if I try," she said "I was telling you the truth when I said you're the one who needs protection. I don't want to hurt you."

They sat quiet for a while. Somehow they had both managed to eat some, but there was still plenty left. Moving the food around was a way to focus on something else.

"Are you angry with me?" she finally asked.

"No, I'm not," he said "But I keep thinking about when you told me, you know that night in the car, that you didn't want to have any regrets. What were you really saying then?"

"I … I regret not giving us a try last year. However at the same time I feel very uncertain about how that would have ended. I guess I thought if we'd tried it, tried us, there's a chance things would have been better between us than they were back then. And we would have been happy for a while. And I don't think I would ever have regretted that, regardless of the pain."

"What makes you so sure it would have ended?"

"I'm not absolutely certain, but … you wanted more from me, than I could give you."

"You think I still do," he concluded.

"Do you get that I'm not saying no? I'm saying not yet," she paused "I think I'm still improving, I'm getting stronger. I still want to work towards that, towards us, I'm just not there yet. Us having sex doesn't change that. The date I wrote on that paper still hasn't passed."

"I know," he said and smiled mischievously.

"You do?" and then she realized what he meant "You peaked," she accused him and batted him on the arm.

"You were practically sticking it up my nose," he laughed at her.

"I was not. You peaked," she repeated.

"I want this," he said seriously "Us. Laughing and bickering. Caring about each other."

"I do too," she said just as seriously and then she leaned forward towards him and looked him straight in the eyes "And at least now we know that once we really get there, the sex will be as satisfying as we thought."

"Bones!" he protested, but she caught the sparkle in his eyes.


	2. Part 2

**No Shortcuts – Part 2**

"Hi," Booth said as he sat down on the chair across from Brennan in the diner "Sorry I'm late."

"It's ok," she smiled "I ordered for you." She had been waiting for 15 minutes for him to show up to their lunch plans.

"Ah, thanks."

"Cam got a match on the DNA we found under victims fingernails. Seems like the husband has some things to explain."

"That's great. Then I'll just do my thing and we can add this one to the solved pile."

"Your thing?" she raised her eyebrows.

"Bones, you know, the thing I do," he put his hands together with a clap "boom, and we have a confession."

"You're quite something," she shook her head.

"So are you," he looked at her suggestively.

"Are you flirting with me?" she asked frankly.

"Maybe I am, but you shouldn't point that out," he laughed

"I like it," she simply said as she looked up at the waitress who just brought by their food. "The flirting I mean, the pointing out I just can't help."

"So what are we doing tonight?" she asked him in between bites.

"Rebecca called and asked if I could take Parker so," he started "Would you still like to come over?"

"Sure. I still owe Parker another chance to beat me at monopoly."

"It's customary to let children win sometimes."

"Then how will he learn?" she said "Besides my dad never let me win."

"Right," he nodded.

ooo

Back at the lab Brennan ran into Angela who was slowly making her way towards Brennan's office.

"Good lunch?" Angela asked. She had brought the sketches and reconstructions she had made on the last case so that Brennan would be able to compile it into evidence.

"Yeah," Brennan said and smiled.

"So when are you going to make it official?" Angela questioned knowing she would probably get the same answer as she had all the times before. Brennan gave her a berating look and as they reached her office she let Angela enter first and then she closed the door.

"Angela," she started to protest.

"Brennan, you told me what happened between you," the other woman cut her off "I didn't force your hand, I didn't pry. And I think that was great. It was about time. So what's going on now?"

"We're not ... There's nothing to make official."

"Why not?" Angela exclaimed impatiently.

"It's not that easy."

Angela slumped down on Brennan's couch and realized she would probably regret it by the time she had to get up.

"But it is that easy. You love each other. You want to be with each other. You," Angela smiled remembering the grin Brennan had had on her face when she told her she'd crawled into bed with Booth "You fit well together. You really shouldn't waste more time."

"I know all that," Brenna nodded "But still … I'm not sure I'll be able to follow through. We've agreed to take things slow. I … I want him in my life, I know that."

"At least you've talked about it."

"Booth and I talk about a lot of things."

"Hm," Angela said, but decided not to remark about all of the talking they had done the previous six years. "You do seem to be doing quite well lately. Maybe you really are moving forward."

ooo

"Do you have a boyfriend?" Parker suddenly asked Brennan. The two of them were sitting at Booth's kitchen table and had just finished their meal of spaghetti with tomato and cheese sauce. Brennan had just gotten to Booth's place when he had gotten a call from the FBI. There was some trouble with the paperwork for the arrest in the case they had been working on and Booth had to go in to make sure all of the i:s were dotted and t:s were crossed. Brennan had insisted that she could stay with Parker at the apartment so Booth didn't have to bring him along to the Hoover-building.

"No," Brennan answered. Usually she liked the straight and to the point questions from Parker, but right now she almost wished that Booth had been there and stopped his son as he probably would have done.

"You want one?"

"I," Brennan hesitated "I don't really know. Why are you asking?"

They were interrupted by the ringing of Booths phone.

"Hello," Parker picked up the phone. "Oh, hi mom," he said after the caller had introduced herself "No, dad isn't here. I'm with Bones," he smiled at Brennan, however the smile was soon vanished from the face. "But you said I could stay here tonight. Dad will be here soon." Parker was quiet for a while and then he finished the call with a quick goodbye. "Mom's coming to pick me up," he told Brennan.

"Was she upset that you were here alone with me?"

"I guess," Parker shrugged and went into his room starting to put his things back into his backpack.

Brennan tried to get a hold of Booth, but he apparently wasn't in his office and his cell went straight to voicemail. She assured Parker that she would tell his father to him as soon as he was home again.

Twenty minutes later there was a knock on the door. Parker went defeatedly to open up and Brennan followed him.

"Hi Rebecca," Brennan said. It had been a long time since the two women had met.

"Hi," Rebecca said briskly "Ready to go, Parker?" she added. She looked rather stressed and angry, but was trying to keep it from her son.

"I guess," Parker turned to Brennan and gave swift wave "Bye."

"Are you sure Parker can't stay?" Brennan said. "Booth will be home soon."

"Yes," Rebecca snapped "I'm quite sure that when I for once ask the father of my child to help out because I need to work late, I expect him to actually be there and take care of his child and not hand him off to his girlfriend or whatever you are."

"I … I," Brennan started to protest.

"Say hi to dad," Parker said before he followed his mother down the stairs.

Shortly after Parker and Rebecca had left Booth called Brennan back and soon he was back in his apartment.

"Did you call Parker?" Brennan asked. She had reheated some of the dinner for Booth as she waited for him to get home. She motioned for Booth to sit down and put down a plate with food in front of him.

"Yes, I called him from the car. He was pretty upset and he said Rebecca was quite rude to you. I'm sorry about that."

"You don't need to apologize for her. Besides I can take it," Brennan said. She had joined him at the table "I feel sorry for Parker though. He wanted to spend time with you. I shouldn't have told you to go without him."

"He was better off staying here with you. I just wish Rebecca could see that."

"Can I ask you something?" Brennan said "Other than what I just did," she added for clarity.

Booth just nodded.

"How come you've never tried any legal action to get more time with him?"

Booth swallowed and looked up at her "Well, even if I don't always agree with the way she does it, Rebecca does what she does out of love for Parker. And I do get to see him enough for us to have a relationship. So even if I want to see him more, and I think he does too, I don't want Parker to be caught in between us fighting any more than is necessary. I hope it will get better when he's older. I don't know if I'm doing the right thing, but hopefully Parker will understand when he's old enough."

"You're doing it for the right reasons and you are a great father," Brennan stated with confidence. "He knows." They continued talking and eventually moved over to the couch. For a while they even got into a rather heated argument about whether or not watching a baseball game would be a meaningful way to spend their Sunday. However from time to time Brennan could feel that Booth's focus was elsewhere.

"I should get home now," Brennan said as she stifled her third yawn "It's getting late."

"You can stay here tonight," he said before adding "Just sleeping."

"Booth …" she protested.

"Yeah, I know," he said "It was worth a try though. I just want to be with you all the time."

Brennan got up and walked over to the door. Booth followed her one step behind. After a quick goodbye and a hug that was just a second longer than what could pass for a partner-hug she went out the door.


	3. Part 3

**No Shortcuts – Part 3**

"I'm pregnant," Brennan finally said as they stopped and faced each other. Booth just looked at her and she had no idea what he was thinking "You're the father;" she added hesitantly. Her words had finally made it all the way in his head and his face broke out in a smile and it was quickly mirrored in hers.

"I know that," he said.

"There's no way you can know …"

"Bones," he interrupted.

"Yeah, ok," she smiled. "Are you ok with this?"

"Oh," he engulfed her with his arms, but then he took a step back and just held his hands around her face wanting to make sure she got every word. "It's the best news I've ever gotten."

"Except for Parker."

"That goes without saying," he laughed "But this goes right up there with him." He brought his arms back around her body and spun her around as he hugged her tightly. "How do you feel?"

"A bit dizzy," she said as her feet were once again on the ground.

"I mean about the baby."

"Oh," she looked down "It's still very early. A lot of pregnancies end in miscarriage." She met his eyes before she added "But since I worry about that, the logical assumption would be that I want this. The pregnancy I mean. And the baby." She smiled at him again and he was quick to respond with a smile as sincere as hers.

Brennan linked her arm with Booth's and they continued walking towards her home.

"When did you find out?" Booth asked.

"I have a very regular menstrual cycle," Brennan said matter of factly "so when my period was late, I kind of suspected it, but I didn't confirm until this morning."

Booth was amazed that she had known all day and he hadn't suspected anything at all while they were working undercover or waiting at the hospital. He guessed that was just another proof of her ability to compartmentalize.

"How do you think this happened?" he asked.

"Booth," she gave him a disbelieving look "You do know how this works, right? The capacitated spermatozoon and the oocyte meet and interact in the ampulla of the fallopian tube," she continued to explain.

"Yeah, yeah I do," he interrupted her "Well not in those words, but I do know how it works. Well I guess nothing's fool proof, huh?" She just gave him a soft smile at that.

"I want us to do this together," Brennan said as they neared her apartment building "I mean I don't want to do this the way I planned."

"You planned?" Booth raised his eyebrows.

"Not this, but two years ago. When I asked for your sperm."

"Oh, right. I remember," he said. That was nothing he was likely to forget about.

"I was going to do it alone, and I'll still do it if …"

"Of course we'll do this together," he put his arm around her so he could pull her even closer as they walked.

"Because this changes everything, right?" she said and looked up at him.

"What do you mean?

"With us. Between us."

He was silent and looked at her trying to figure out what she was thinking.

"Well, we'll be together," she said all of sudden feeling insecure about the statement "Because of the baby."

"You want us to be in a relationship because of the baby."

"Yes," she simply said.

"And if you weren't pregnant?" he had to ask.

"That scenario poses infinite possibilities."

"I … I …" he didn't know what to say or where to start "I need to take a walk, clear my head … You go on up, I'll be right with you." Booth felt like all of the information he had gotten in the last half hour was finally catching up with him and he didn't know what to make of it. He could see that Brennan was reluctant to let him walk away, but finally she nodded and walked towards the entrance of her apartment building. Once she was safely inside he turned around and walked towards the park nearby.

It was almost half an hour later that Booth knocked on her door. She came and unlocked the door and then just went back to her dining room table. On it were a large stack of papers her grad students had written. She went back to looking at the page before her, highlighted a paragraph and scribbled down something in the marginal.

"Bones, we need to talk," Booth said, he had followed her into her living room.

"I need to finish this paper now or I'll have to start all over again," she answered and continued working silently turning a page over once in a while. Booth sat down on the armchair, his usual spot, and waited patiently. He knew this was her way of gathering her thoughts. Eventually she put the pen down and turned on the chair to face him. Her face was rather stiff and he couldn't really tell what she was thinking.

"Bones," he started again "I'm sorry I walked away." At first he thought that she wasn't going to join him by the couch, but she got up and walked over to sit down. She looked at him and he could tell he had her full attention when he continued "Of course we'll do this together if that's what you want. You have to know that. You know what kind of man I am. I just never thought that would be us. I don't want that to be us."

"I thought a relationship would be what _you_ wanted," she said "I've seen what it's like for you with Parker. I don't want to cause you that kind of pain. With the pregnancy, that's just the best way I can think of to prevent that from happening."

"After everything that has happened between us, especially the last couple of months, I can't believe you'd say you want us to be together just because we're having a child together. It's not a good enough reason," he was getting agitated. This day had been real rollercoaster of emotions between the thrill of being undercover investigating the case at the bowling alley, the anxiousness when they were waiting for their friends child to be born and the relief knowing he was fine, the joy at her announcement and now the anger and frustration because everything that had been going in the right direction was in some way taking a turn for the worse.

"I want you to _want_ to be with me because it's what _you_ want, not because that's what you think _I_ want … you to want," he concluded. This was more complicated than it should have to be.

They were both quiet and looked deep into each other's eyes, almost daring the other to not be the first to look away.

"What exactly is it you want from me? From this relationship?" she spoke and her voice was much calmer than his. He could tell that her analytical brain was trying to solve this as an especially complicated problem.

"I want to share everything with you. The good, the bad and the ugly. To be there for you no matter what happens. And love," it was hard for him to put it into words, but he knew she needed it literarily spelled out.

"And sex," Brennan added.

He gave her an intense look "To make love to you, yes," he nodded.

"I've shared more with you than anyone else," she started talking again "We know everything about each other and I can think of nothing that I wouldn't do for you. I came to the conclusion that I love you a long time ago. So what you're really saying is that the only thing that would have to change is that we'd also have physical relationship. On a regular basis, I mean."

He could see her point, but he would never have expressed or even thought about it like that. She got up from her spot on the couch and took the few steps that were required to reach the armchair where he was sitting. She sat down on his lap, straddling him with one leg on either side of him. "Because I could definitely agree to that," she said seductively and bent down to kiss him. He was caught by surprise by her actions and couldn't help himself but for a second get lost in the moment and kiss her back.

"No," he finally got out and he put his hand on her shoulders to just slightly push her away a few inches away.

"No?" she said and looked him in the eyes. In one swift motion she was back at her spot of the couch. He followed her and sat down beside her. He reached for her hand and even though she tried to pull away, he held on to it.

"I want you. I every possible way," he said hoping she would never ever doubt that "I just don't want a friend's death to be the reason we crossed that line the first time, just as I don't want an unexpected pregnancy to be the ultimate reason why we're in a relationship," he was finally putting into words what he had been worrying about ever since that night. "What we have is so much more than that. I want you to be sure it is what you want right now," he concluded.

"It is," she told him "But don't you see? If it had been any other person in that bedroom, I would never have gotten into it. I was upset and I went to you. For me that's special and unique in its own way. What I have with you, I've never had with anyone else." She was looking into his eyes, no longer trying to pull away.

"So what you're saying is that it's more important that it happened with the right person, than the specifics of how and why it happened."

"I think that's how you would put it." She moved her hand up towards his face and tenderly stroked him. He moved his face closer to hers and their lips met in a sweet yet cautious kiss. He pulled her closer into a hug so that she was sitting with her legs across his lap and she buried her face against his neck. They remained in the same position enjoying the close proximity of both body and mind. Booth put a hand to her flat stomach and Brennan smiled and decided against pointing out to him there was nothing to feel there yet. Maybe they weren't done trying to define their relationship, maybe they never would be, but they were done for now.

"I need food," Brennan broke the silence.

"You want to stay in?"

"Yeah," she nodded "I have some leftovers in the fridge we can heat up."

"We can't eat reheated take out," Booth protested.

"Why not?" she had already gotten to her feet and was walking over to the kitchen with Booth following her.

"Because it's not," he paused "festive enough for the occasion. Let's at least get something new. I'm thinking Lebanese"

"It would be wasteful to just throw it away," she protested. They were both working around the kitchen, her taking out the leftovers from the fridge and him looking for the take-out menu from that Lebanese place they had tried a couple of weeks back. He eventually realized he was defeated since she'd probably be done before he had even placed the call.

"Tomorrow I'm taking you out to dinner to celebrate," he promised and started help her get everything in order.

"What are we celebrating?" Brennan asked trying her best to sound oblivious.

"Seriously?" Booth looked at her "Oh, you're joking," he realized when he saw the look on her face "That wasn't funny," he berated her and used his long arms to tickle her side furthest from him so she had no choice but to move into his embrace.

"Then why are you smiling?"

**The End**

**AN:** Thank you to everyone that responded by review, putting it among your favorites or story alerts! It's very nice to know there's some people out there reading and even more so when I'm told what you think of it.


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